36CR | pdb_000036cr

Structure of the Evo-Phi36 bacteriophage

• PDB DOI: https://doi.org/10.2210/pdb36CR/pdb
• EM Map EMD-77391: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Sinsheimervirus
• Expression System: Escherichia coli C
• Mutation(s): No 


• Deposited: 2026-06-01 Released: 2026-07-08 
• Deposition Author(s): Li, D.B., King, S.H., Driscoll, C.L., Wilkinson, M.E., Hie, B.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Generative design of bacteriophages with genome language models.

King, S.H., Driscoll, C.L., Li, D.B., Guo, D., Merchant, A.T., Brixi, G., Wilkinson, M.E., Hie, B.L.

(2026) Science 393: eaec2657-eaec2657

• PubMed: 42561074 
• DOI: https://doi.org/10.1126/science.aec2657
• Primary Citation Related Structures: 
  36CQ, 36CR


• PubMed Abstract: 
  

  Many important biological functions arise not from single genes but from complex interactions encoded by entire genomes. We report the first generative design of complete bacteriophage genomes using genome language models. We generated viable bacteriophages with target host tropism, using the phage ΦX174 as our design template. Experimental testing yielded 16 phages with diverse fitness profiles in laboratory conditions. Cryo-electron microscopy confirmed that a generated phage utilizes an evolutionarily distant DNA packaging protein in its capsid. A cocktail of generated phages rapidly overcomes ΦX174-resistant Escherichia coli strains, demonstrating a path toward artificial intelligence-generated phage therapies against rapidly evolving bacterial pathogens. This work provides a blueprint for the design of diverse synthetic bacteriophages and useful biological systems at the genome scale.

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Organizational Affiliation: 
• Department of Bioengineering, Stanford University, Stanford, CA, USA.
Arc Institute, Palo Alto, CA, USA.
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Stanford Data Science, Stanford University, Stanford, CA, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 180-mer - A60B60C60 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 180-mer - AA60AB60AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 70.41 kDa 
• Atom Count: 4,849 
• Modeled Residue Count: 612 
• Deposited Residue Count: 627 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein J	A	25	Sinsheimervirus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein F	B	427	Sinsheimervirus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Major spike protein G	C	175	Sinsheimervirus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
RECONSTRUCTION	RELION	5.0
MODEL REFINEMENT	PHENIX	2.0_5936

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-08 
Deposition Author(s): Li, D.B., King, S.H., Driscoll, C.L., Wilkinson, M.E., Hie, B.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-07-08
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Changes: Data collection, Database references
• Version 1.2: 2026-08-19
  Changes: Data collection, Database references